Defence Minister David Johnston says he is extremely angry about the ABC's coverage of stories about the navy's treatment of asylum seekers, saying he has not commented before now because he needed time to cool off.

Last week ABC managing director Mark Scott said the initial reporting of the mistreatment claims needed more precise wording, and expressed regret if it led anyone to assume the ABC supported the claims.

Today Defence Minister David Johnston said the ABC had maliciously maligned Navy personnel, who he described as heroes.

"The good men and women of the Royal Australian Navy have been maliciously maligned by the ABC and I am very dissatisfied with the weasel words of apology that have been floated around by senior management of the ABC," he said.

The Defence Minister said Customs and the Navy had saved "thousands of lives" between Christmas Island and Java over the last four years.

"My people have been spat on, abused, treated like servants, and have endured all of that to save more than a thousand lives, and yet they've also had to endure the horror of fishing out hundreds of people floating dead in the water," he said.

"I am absolutely sick to the stomach that this Australian iconic news agency would attack the Navy in the way that it has."

He described the Navy as "heroes", and called for an investigation into the ABC.

"If ever there was an event that justified a detailed inquiry, some reform, an investigation of the ABC, this event is it," he said.

"They themselves have cast a giant shadow over the veracity of their reporting and yet they've besmirched these hard-working people."

Senator Johnston says he has spoken to senior command and they have assured him that there is no substance to the allegations that asylum seekers have been mistreated.

A spokesman for ABC managing director Mark Scott has told The World Today that he will not be making any comment about Senator Johnston's comments.

"Let's get a bit real here and give somebody a bit of natural justice please.

"Let's see the allegations first, let's have more than just rumour, innuendo, and hearsay please.

"When you give me something to act upon that is more than just hearsay, innuendo and rumour we'll cross that bridge when we come to it."

Senator Johnston was asked about allegations in Fairfax papers today, including that the Navy turned off the lights on boats.

In response he asked "why would you view the glass half empty at every point?"

"I'm not aware of operational matters, you need to put that to Border Protection Command," he said.

"I have the greatest confidence in these people.

"I've travelled for a week on board an Armidale-class patrol boat, I've seen the level of professionalism.

"I'm backing them at every turn of every corner."

And the Defence Minister defended his lack of knowledge about the operations.

"On-water matters in this area, as I've tried to explain to you, are a civil public policy outcome," he said.

PM rejects call to release video of operations

Prime Minister Tony Abbott has rejected calls for the Navy to release photos or videos to show exactly what has happened during operations to intercept asylum seekers.

He says he does not want to do anything that would cast aspersions on the professionalism of naval or Customs personnel.

"I have nothing but respect for them. They are doing a fine job, often under difficult circumstances. They act in accordance with the humanity which you would expect of Australian military and service personnel and I have seen nothing that credibly casts doubts upon that professionalism."

Asked if releasing footage could dispel ambiguity, Mr Abbott said it might also help people smugglers.

The Prime Minister also played down suggestions that the asylum seeker issue is inflaming tensions with Indonesia.

"I have nothing but respect and admiration for president (Susilo Bambang) Yudhoyono, who has not only been a great president of Indonesia, but he has been a very good friend to Australia," he said.

"The important thing here for both our countries is to stop the boats and I'm very pleased to note that today is the 50th day without an illegal boat arriving in Australia.

"I think you've got to go back to 2008 before you had a period like that.

"So, these policies are working.

"Yes, they are tough policies, but they are working."

Mr Abbott again criticised the ABC's coverage of the story, saying that allegations of such seriousness made by someone with such self-interest should have been corroborated before they were broadcast.

Shorten accuses Government of 'hiding behind' military

Federal Opposition leader Bill Shorten says the Government is setting the military up to fail by insisting on secrecy about asylum seeker interceptions.

In a comment likely to infuriate the Government, he has accused it of hiding behind the military uniforms.

Mr Shorten says the Government should be open with the Australian people and is not helping the military by refusing to comment on operations.

"The Navy do a tough job but their job is made even tougher when you've got a Federal Government hiding behind the uniforms not standing up for them," he said.

"What we need here is to forget the secrecy. The Australian people will give a fair bit of slack to governments provided they are up front with the Australian people. It's time to end the secrecy - and its time to stop leaving our Navy out on their own."

The Opposition Leader also lashed out at Immigration Minister Scott Morrison's approach.

"What stuns me is that the Minister for Immigration is happy to add to his scrapbook collection with cute photos of him on a boat and yet at the same time the Navy has got to undergo allegations, rumour and innuendo.

"What would help our military forces is for our elected representatives, the Abbott Government, to stop hiding behind operational secrecy. Just be straight with the Australian people. That is the best solution, rather than letting the Navy get embroiled in issues because the Abbott Government isn't strong enough to stand up and be transparent on their policies."

"What's frustrating for Australians, [for] people trying to report the news for Australians, [for] people concerned about our good name, and also for those who love and support our military forces, is that you can find out more about what Australia is doing in the Indonesian newspapers.

"It is not good enough for the Abbott Government to only come into sight when they've got a photo opportunity and then disappear like a submarine on every other issue."

Mr Shorten refused to comment on allegations against Defence and Customs, instead assuring them that Labor supports the military.

"I just want the families of our service people who are doing this tough job to know that the Labor party respects the contribution that your loved ones are making for us. We're certainly not leaping to any conclusions."